4g8b - Revision history

OCA at 13:56, 8 November 2023

2023-11-08T13:56:45Z

←Older revision		Revision as of 13:56, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4g8b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ochrobactrum_sp._T63 Ochrobactrum sp. T63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G8B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4g8b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ochrobactrum_sp._T63 Ochrobactrum sp. T63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G8B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HL6:N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE'>HL6</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.302Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HL6:N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE'>HL6</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [https://pdbe.org/4g8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [https://www.ebi.ac.uk/pdbsum/4g8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g8b ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [https://pdbe.org/4g8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [https://www.ebi.ac.uk/pdbsum/4g8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g8b ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:41, 26 October 2022

2022-10-26T06:41:33Z

←Older revision		Revision as of 06:41, 26 October 2022
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	==Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone==		==Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone==
-	<StructureSection load='4g8b' size='340' side='right' caption='[[4g8b]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='4g8b' size='340' side='right'caption='[[4g8b]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4g8b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ochrobactrum_sp.~~_t63~~ Ochrobactrum sp. ~~t63~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4G8B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4g8b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ochrobactrum_sp._T63 Ochrobactrum sp. T63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G8B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HL6:N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE'>HL6</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HL6:N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE'>HL6</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g5x\|4g5x]], [[4g8c\|4g8c]], [[4g8d\|4g8d]], [[4g9e\|4g9e]], [[4g9g\|4g9g]]</td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [https://pdbe.org/4g8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [https://www.ebi.ac.uk/pdbsum/4g8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g8b ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aidH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680275 Ochrobactrum sp. T63])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [~~http~~://pdbe.org/4g8b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4g8b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4g8b ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D2J2T6_9HYPH D2J2T6_9HYPH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ochrobactrum sp. ~~t63~~]]	+	[[Category: Large Structures]]
-	[[Category: Gao, A]]	+	[[Category: Ochrobactrum sp. T63]]
-	[[Category: Liang~~, D C~~]]	+	[[Category: Gao A]]
-	[[Category: Yan~~, X X]]~~	+	[[Category: Liang DC]]
-	~~[[Category: Ahl]]~~	+	[[Category: Yan XX]]
-	~~[[Category: Ahl-lactonase]]~~	+
-	~~[[Category: Alpha/beta-hydrolase fold]]~~	+
-	~~[[Category: Cap-domain]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 19:53, 15 December 2016

2016-12-15T19:53:24Z

←Older revision		Revision as of 19:53, 15 December 2016
Line 1:		Line 1:
		+
	==Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone==		==Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone==
	<StructureSection load='4g8b' size='340' side='right' caption='[[4g8b]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4g8b' size='340' side='right' caption='[[4g8b]], [[Resolution\|resolution]] 1.30Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g5x\|4g5x]], [[4g8c\|4g8c]], [[4g8d\|4g8d]], [[4g9e\|4g9e]], [[4g9g\|4g9g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g5x\|4g5x]], [[4g8c\|4g8c]], [[4g8d\|4g8d]], [[4g9e\|4g9e]], [[4g9g\|4g9g]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aidH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680275 Ochrobactrum sp. T63])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aidH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680275 Ochrobactrum sp. T63])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [http://www.ebi.ac.uk/pdbsum/4g8b PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [http://pdbe.org/4g8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [http://www.ebi.ac.uk/pdbsum/4g8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g8b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4g8b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:19, 10 December 2014

2014-12-10T09:19:06Z

←Older revision		Revision as of 09:19, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4g8b.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone==
		+	<StructureSection load='4g8b' size='340' side='right' caption='[[4g8b]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4g8b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_sp._t63 Ochrobactrum sp. t63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G8B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HL6:N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE'>HL6</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g5x\|4g5x]], [[4g8c\|4g8c]], [[4g8d\|4g8d]], [[4g9e\|4g9e]], [[4g9g\|4g9g]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aidH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680275 Ochrobactrum sp. T63])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4g8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g8b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g8b RCSB], [http://www.ebi.ac.uk/pdbsum/4g8b PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many pathogenic bacteria that infect humans, animals and plants rely on a quorum-sensing (QS) system to produce virulence factors. N-Acyl homoserine lactones (AHLs) are the best-characterized cell-cell communication signals in QS. The concentration of AHL plays a key role in regulating the virulence-gene expression and essential biological functions of pathogenic bacteria. N-Acyl homoserine lactonases (AHL-lactonases) have important functions in decreasing pathogenicity by degrading AHLs. Here, structures of the AHL-lactonase from Ochrobactrum sp. (AidH) in complex with N-hexanoyl homoserine lactone, N-hexanoyl homoserine and N-butanoyl homoserine are reported. The high-resolution structures together with biochemical analyses reveal convincing details of AHL degradation. No metal ion is bound in the active site, which is different from other AHL-lactonases, which have a dual Lewis acid catalysis mechanism. AidH contains a substrate-binding tunnel between the core domain and the cap domain. The conformation of the tunnel entrance varies with the AHL acyl-chain length, which contributes to the binding promiscuity of AHL molecules in the active site. It also supports the biochemical result that AidH is a broad catalytic spectrum AHL-lactonase. Taken together, the present results reveal the catalytic mechanism of the metal-independent AHL-lactonase, which is a typical acid-base covalent catalysis.

-	~~{{STRUCTURE_4g8b\| PDB=4g8b \| SCENE= }}~~	+	High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase.,Gao A, Mei GY, Liu S, Wang P, Tang Q, Liu YP, Wen H, An XM, Zhang LQ, Yan XX, Liang DC Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):82-91. doi:, 10.1107/S0907444912042369. Epub 2012 Dec 20. PMID:23275166<ref>PMID:23275166</ref>

-	~~===Crystal structures~~ of ~~N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23275166}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4g8b]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Ochrobactrum_sp._t63 Ochrobactrum sp. t63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA].~~	+	</StructureSection>
	[[Category: Ochrobactrum sp. t63]]		[[Category: Ochrobactrum sp. t63]]
-	[[Category: Gao, A.]]	+	[[Category: Gao, A]]
-	[[Category: Liang, D C.]]	+	[[Category: Liang, D C]]
-	[[Category: Yan, X X.]]	+	[[Category: Yan, X X]]
	[[Category: Ahl]]		[[Category: Ahl]]
	[[Category: Ahl-lactonase]]		[[Category: Ahl-lactonase]]

OCA at 08:48, 16 January 2013

2013-01-16T08:48:50Z

←Older revision		Revision as of 08:48, 16 January 2013
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-	~~'''Unreleased structure'''~~	+	[[Image:4g8b.jpg\|left\|200px]]

-	~~The entry~~ 4g8b ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4g8b\| PDB=4g8b \| SCENE= }}

-	~~Authors: Liang, D.C., Yan, X.X., Gao, A.~~	+	===Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone===

-	~~Description~~: ~~Crystal structures of N~~-~~acyl homoserine~~ lactonase ~~AidH S102G mutant complexed with N~~-~~hexanoyl homoserine lactone~~	+	{{ABSTRACT_PUBMED_23275166}}
		+
		+	==About this Structure==
		+	[[4g8b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_sp._t63 Ochrobactrum sp. t63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G8B OCA].
		+	[[Category: Ochrobactrum sp. t63]]
		+	[[Category: Gao, A.]]
		+	[[Category: Liang, D C.]]
		+	[[Category: Yan, X X.]]
		+	[[Category: Ahl]]
		+	[[Category: Ahl-lactonase]]
		+	[[Category: Alpha/beta-hydrolase fold]]
		+	[[Category: Cap-domain]]
		+	[[Category: Hydrolase]]

OCA at 05:31, 22 August 2012

2012-08-22T05:31:38Z

←Older revision		Revision as of 05:31, 22 August 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4g8b is ON HOLD	+	The entry 4g8b is ON HOLD until Paper Publication

	Authors: Liang, D.C., Yan, X.X., Gao, A.		Authors: Liang, D.C., Yan, X.X., Gao, A.

-	Description: Crystal structures ~~of AidH complexes provide insights into a novel catalytic mechanism~~ of N-acyl homoserine lactonase	+	Description: Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone

OCA at 05:23, 15 August 2012

2012-08-15T05:23:11Z

←Older revision		Revision as of 05:23, 15 August 2012
Line 3:		Line 3:
	The entry 4g8b is ON HOLD		The entry 4g8b is ON HOLD

-	Authors: Liang, D.C, Yan, X.X, Gao, A	+	Authors: Liang, D.C., Yan, X.X., Gao, A.

	Description: Crystal structures of AidH complexes provide insights into a novel catalytic mechanism of N-acyl homoserine lactonase		Description: Crystal structures of AidH complexes provide insights into a novel catalytic mechanism of N-acyl homoserine lactonase

OCA: Protected "4g8b" [edit=sysop:move=sysop]

2012-08-01T05:30:30Z

Protected "4g8b" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 1 August 2012

OCA: New page: '''Unreleased structure''' The entry 4g8b is ON HOLD Authors: Liang, D.C, Yan, X.X, Gao, A Description: Crystal structures of AidH complexes provide insights into a novel catalytic mec...

2012-08-01T05:30:28Z

New page: '''Unreleased structure''' The entry 4g8b is ON HOLD Authors: Liang, D.C, Yan, X.X, Gao, A Description: Crystal structures of AidH complexes provide insights into a novel catalytic mec...

New page

'''Unreleased structure'''

The entry 4g8b is ON HOLD

Authors: Liang, D.C, Yan, X.X, Gao, A

Description: Crystal structures of AidH complexes provide insights into a novel catalytic mechanism of N-acyl homoserine lactonase